Computational structured illumination for high-content fluorescent and phase microscopy

High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use speckle structured illumination microscopy (SIM) as a robust and cost-effective solution for high-content fluorescence microscopy with simultaneous high-content quantitative phase (QP). This multi-modal compatibility is essential for studies requiring cross-correlative biological analysis. Our method uses laterally-translated Scotch tape to generate high-resolution speckle illumination patterns across a large FOV. Custom optimization algorithms then jointly reconstruct the sample's super-resolution fluorescent (incoherent) and QP (coherent) distributions, while digitally correcting for system imperfections such as unknown speckle illumination patterns, system aberrations and pattern translations. Beyond previous linear SIM works, we achieve resolution gains of 4x the objective's diffraction-limited native resolution, resulting in 700 nm fluorescence and 1.2 um QP resolution, across a FOV of 2x2.7 mm^2, giving a space-bandwidth product (SBP) of 60 megapixels

Structured illumination microscopy with unknown patterns and a statistical prior

Structured illumination microscopy (SIM) improves resolution by down-modulating high-frequency information of an object to fit within the passband of the optical system. Generally, the reconstruction process requires prior knowledge of the illumination patterns, which implies a well-calibrated and aberration-free system. Here, we propose a new \textit{algorithmic self-calibration} strategy for SIM that does not need to know the exact patterns {\it a priori}, but only their covariance. The algorithm, termed PE-SIMS, includes a Pattern-Estimation (PE) step requiring the uniformity of the sum of the illumination patterns and a SIM reconstruction procedure using a Statistical prior (SIMS). Additionally, we perform a pixel reassignment process (SIMS-PR) to enhance the reconstruction quality. We achieve 2$\times$ better resolution than a conventional widefield microscope, while remaining insensitive to aberration-induced pattern distortion and robust against parameter tuning

Content-Based Weak Supervision for Ad-Hoc Re-Ranking

One challenge with neural ranking is the need for a large amount of manually-labeled relevance judgments for training. In contrast with prior work, we examine the use of weak supervision sources for training that yield pseudo query-document pairs that already exhibit relevance (e.g., newswire headline-content pairs and encyclopedic heading-paragraph pairs). We also propose filtering techniques to eliminate training samples that are too far out of domain using two techniques: a heuristic-based approach and novel supervised filter that re-purposes a neural ranker. Using several leading neural ranking architectures and multiple weak supervision datasets, we show that these sources of training pairs are effective on their own (outperforming prior weak supervision techniques), and that filtering can further improve performance.Comment: SIGIR 2019 (short paper

Non visual effects of light: an overview and an Italian experience

Since the discovery of non-visual effect of light, consequences on human psychology and physiology have been investigated; however, effects on cognition of exposure to different spectral composition have been partially explored. Aim of this paper is an overview on researches developed in this field to compare general approaches and measurements protocols: the scarce knowledge of the physiological mechanisms, as well as the lack of shared methods, techniques, tools and procedures represent the weak point of this research. The impact of different procedures and experimental settings on results is shown, evidencing the need for scientifically consistent and internationally agreed procedures

An Automated Treatment Plan Quality Control Tool for Intensity-Modulated Radiation Therapy Using a Voxel-Weighting Factor-Based Re-Optimization Algorithm.

Intensity-modulated radiation therapy (IMRT) currently plays an important role in radiotherapy, but its treatment plan quality can vary significantly among institutions and planners. Treatment plan quality control (QC) is a necessary component for individual clinics to ensure that patients receive treatments with high therapeutic gain ratios. The voxel-weighting factor-based plan re-optimization mechanism has been proved able to explore a larger Pareto surface (solution domain) and therefore increase the possibility of finding an optimal treatment plan. In this study, we incorporated additional modules into an in-house developed voxel weighting factor-based re-optimization algorithm, which was enhanced as a highly automated and accurate IMRT plan QC tool (TPS-QC tool). After importing an under-assessment plan, the TPS-QC tool was able to generate a QC report within 2 minutes. This QC report contains the plan quality determination as well as information supporting the determination. Finally, the IMRT plan quality can be controlled by approving quality-passed plans and replacing quality-failed plans using the TPS-QC tool. The feasibility and accuracy of the proposed TPS-QC tool were evaluated using 25 clinically approved cervical cancer patient IMRT plans and 5 manually created poor-quality IMRT plans. The results showed high consistency between the QC report quality determinations and the actual plan quality. In the 25 clinically approved cases that the TPS-QC tool identified as passed, a greater difference could be observed for dosimetric endpoints for organs at risk (OAR) than for planning target volume (PTV), implying that better dose sparing could be achieved in OAR than in PTV. In addition, the dose-volume histogram (DVH) curves of the TPS-QC tool re-optimized plans satisfied the dosimetric criteria more frequently than did the under-assessment plans. In addition, the criteria for unsatisfied dosimetric endpoints in the 5 poor-quality plans could typically be satisfied when the TPS-QC tool generated re-optimized plans without sacrificing other dosimetric endpoints. In addition to its feasibility and accuracy, the proposed TPS-QC tool is also user-friendly and easy to operate, both of which are necessary characteristics for clinical use